splitncigar

Accelerated SplitNCigarReads functionality from GATK. This tool splits reads that contain Ns in their cigar string (e.g. spanning splicing events in RNAseq data).

Quick Start

$ pbrun splitncigar \
    --ref Ref.fa \
    --in-bam in.bam \
    --out-bam out.bam

Compatible GATK Command

The commands below are the GATK counterpart of the Parabricks command above. The output from these commands will be identical to the output from the above command.

gatk SplitNCigarReads --reference Ref.fa --input in.bam --output tmp.bam

gatk SortSam --java-options -Xmx30g --MAX_RECORDS_IN_RAM=5000000 -I=tmp.bam \
    -O=out.bam --SORT_ORDER=coordinate --TMP_DIR=/raid/myrun

splitncigar Reference

Split reads in a BAM file that contain Ns in their cigar string.

Input/Output file options

--ref REF

Path to the reference file. (default: None)

Option is required.

--in-bam IN_BAM

Path to the BAM file. (default: None)

Option is required.

--knownSites KNOWNSITES

Path to a known indels file. The file must be in vcf.gz format. This option can be used multiple times. (default: None)

--out-bam OUT_BAM

Output BAM file. (default: None)

Option is required.

--out-recal-file OUT_RECAL_FILE

Path of the report file after Base Quality Score Recalibration. (default: None)

Tool Options:

--num-cpu-threads NUM_CPU_THREADS

Number of CPU threads to traverse separate chromosomes in splitncigar. (default: 6)

--no-ignore-mark

Do not ignore marked reads in sorted output. (default: None)

Common options:

--logfile LOGFILE

Path to the log file. If not specified, messages will only be written to the standard error output. (default: None)

--tmp-dir TMP_DIR

Full path to the directory where temporary files will be stored.

--with-petagene-dir WITH_PETAGENE_DIR

Full path to the PetaGene installation directory. By default, this should have been installed at /opt/petagene. Use of this option also requires that the PetaLink library has been preloaded by setting the LD_PRELOAD environment variable. Optionally set the PETASUITE_REFPATH and PGCLOUD_CREDPATH environment variables that are used for data and credentials (default: None)

--keep-tmp

Do not delete the directory storing temporary files after completion.

--license-file LICENSE_FILE

Path to license file license.bin if not in the installation directory.

--no-seccomp-override

Do not override seccomp options for docker (default: None).

--version

View compatible software versions.

GPU options:

--num-gpus NUM_GPUS

Number of GPUs to use for a run. GPUs 0..(NUM_GPUS-1) will be used.

--gpu-devices GPU_DEVICES

GPU devices to use for a run. By default, all GPU devices will be used. To use specific GPU devices, enter a comma-separated list of GPU device numbers. Possible device numbers can be found by examining the output of the nvidia-smi command. For example, using --gpu-devices 0,1 would only use the first two GPUs.